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# Performs PWM scanning with TRANSFAC and JASPAR matrices and filters out matches that show no phylogenetic conservation
#

DNA = new DNA sequence dataset(DataTrack:DNA)
Multiz28wayCons = new Numeric dataset(DataTrack:Multiz28wayCons)
TRANSFAC_Public = new Motif Collection(Collection:TRANSFAC Public)
Jaspar_Core = new Motif Collection(Collection:Jaspar Core)
AllMotifs = new Motif Collection(TRANSFAC_Public,Jaspar_Core)
bgmodel = new Background Model(Model:EPD_human_3)
prompt bgmodel "Select background model"
threshold = new Numeric Variable(7.0)
prompt threshold "Select PWM threshold"
BindingSites = motifScanning on DNA with SimpleScanner {Motif Collection=AllMotifs,Background=bgmodel,Threshold=threshold}
filter BindingSites where region average Multiz28wayCons < 0.2